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In Palermo, Italy in 1979, Fabbrizio Disguisey, the latest in a long line of Italian secret agents known as "Masters of Disguise", breaks up a smuggling ring run by the evil Devlin Bowman but barely avoids getting caught (while disguised as Bo Derek). Bowman is arrested and Fabbrizio decides it best to keep his family's identity a secret from his infant son, Pistachio.

Twenty-three years later, Fabbrizio runs an Italian restaurant in America with his unnamed wife and Pistachio working as, respectively, the cook and a waiter. Thanks to his yet-untold family heritage, Pistachio has a tendency to mock people at random, which are annoying and badly timed impersonations. He's also looking for a wife that has a large rear like his mother, but his nerdy demeanor makes him unlikeable to women, as well as a target for bullies, like fellow waiter Rex.

One night, Devlin Bowman, fresh out of jail, kidnaps Fabbrizio and "Mama", forcing the former to use his Disguisey powers to steal legendary artifacts like the U.S. Constitution, the Liberty Bell, and the Apollo 11 Lunar Module while disguised as track runner Michael Johnson, Governor Jesse Ventura, and famous singer Jessica Simpson while also threatening to harm his wife, who is brainwashed to not notice anything. Shortly after Fabbrizio's disappearance, Pistachio is visited by his unnamed grandfather, who reveals Pistachio's heritage and begins training him in the ways of becoming a Master of Disguise.

Eventually, Pistachio gets the basics of the Disguisey way down and his grandfather gets him an assistant, the gorgeous (but small-bottomed) Jennifer Baker, while he has bonded with her son Barney who is trying to learn how to ride a skateboard and becomes attached to Pistachio's dog The Cuteness, and who is a little confused about what the job entails. The two search the area where Fabbrizio was kidnapped and find one of Bowman's cigars, which is emblazoned with the symbol of the "Turtle Club". To get into the club, Pistachio disguises himself as a man who dresses and acts like a turtle and ends up embarrassing himself and Jennifer. They manage to learn Bowman's name and scheme, as well as that he'll be at an antiques fair the next day.

Pistachio and Jennifer go to the fair, with Pistachio disguised as an elderly woman named Gammy Num-Nums. Pistachio (Gammy Num-Nums) remarks many things to Bowman, such as "You're a tall glass of water, and I just love moisture!" and "We're never going to make babies!". Bowman, ignoring Gammy Num-Nums, invites Jennifer to a party at his house. Pistachio goes to the party disguised as Mr. Peru and starts bugging Bowman (and his waiter, too) while Jennifer looks for clues. Pistachio, as Mr. Peru, gets so much into his character, that he starts dancing on stage. Though Jennifer gets the images, Pistachio causes so much trouble that he's forced to abandon Jennifer when Bowman sends his men after him. Pistachio loses the henchmen by disguising himself as shark-hunter Quint and a large cow pie. He uses other disguises, like Bavarian tax agent Constable Mueller and British secret agent Terry Suave, to get Jennifer to safety.

That night, Pistachio and Jennifer look through the clues at a local restaurant, and they deduce that Bowman has forced Fabbrizio to go back to his disguising ways to steal the treasures for Bowman. While there, they find Jennifer's boyfriend Trent cheating on her by being out on a date with Pistachio's former love interest Sophia, who was also involved with Rex. Pistachio then ends up slapping him into submission (after learning moves from his slapping dummy), then leaving with the love-struck Jennifer.

Pistachio takes Jennifer home, when Jennifer kisses Pistachio, leaving him love-struck. Bowman's men kidnap Jennifer as soon as Pistachio leaves and Jennifer is in her home. Barney finds Pistachio talking with his grandfather via pre-recorded hologram and a plan is formed. Pistachio, after hiding in a cherry pie and disguised as a "Cherry Pie Man," breaks into Bowman's house to rescue Jennifer and his parents and stops the auction. But even after defeating Bowman's ninja army, Bowman has one final trick up his sleeve: he has attached a mask of his own face to Fabbrizio's head, making him appear to be Bowman. While the real Bowman escapes, Pistachio is forced to fight his father, who is brainwashed to believe he is Bowman. Grandfather soon arrives to witness Pistachio obtain his first victory.

In the end, Pistachio helps his father snap out his trance by showing off the old habit of putting his underwear on his head, they free "Mama", return the artifacts, Pistachio marries Jennifer, becomes Barney's stepfather and becomes an official Master of Disguise. However, there is one final thing to deal with — Bowman still has the Constitution. Luckily, the Disguiseys locate him in Costa Rica. Disguised as George W. Bush, Pistachio, along with Fabbrizio and his grandfather (who disguised themselves as Bowman's henchmen) defeat Bowman once and for all and retrieve the Constitution.

Over the end credits, we see numerous out-takes, deleted scenes, musical numbers and the characters partying along to the soundtrack in between credits. We also see Jennifer dressed in a bridal gown, proving that she was married, or engaged, to Pistachio.

After the end credits finally end, while Pistachio is cleaning up his restaurant, he discovers that a dwarfed man who resembles Mario was in the slapping dummy the whole time. Then the dwarfed man chases him. The two have a conversation and say goodbye. Then so does The Cuteness who reveals himself to have been Pistachio's grandfather all along.

The film was universally panned by critics, many of whom considered the plot sophomoric, compounding the fact that there were several disguises that would clearly not be recognized by children (Tony Montana from Scarface, for example).

As of March 2007, review-aggregation website Rotten Tomatoes ranked the film as the 18th worst-reviewed of the 00's decade, with a 1% rating, and its consensus reading: "An ill-conceived attempt to utilize Dana Carvey's talent for mimicry, The Master of Disguise is an irritating, witless farce weighted down by sophomoric gags."[4] On Metacritic, the film scored 12 out of 100, indicating "Overwhelming Dislike".[5] Comedian and former Mystery Science Theater 3000 host Michael J. Nelson named the film the third-worst comedy ever made.[6]